Kaposi sarcoma (KS) is the most common HIV-associated malignancy worldwide and causes significant morbidity and mortality, particularly in sub-Saharan Africa. Human herpesvirus-8 (HHV-8) is the etiologic agent of KS, but the natural history of progression from asymptomatic HHV-8 infection to KS development is poorly understood. Viral genomic diversity plays an important role in the risk of cancer and response to treatment in some oncogenic viruses, but HHV-8 genomic heterogeneity has been described in only limited regions of the viral genome and the potential contribution of HHV-8 diversity to KS pathogenesis and treatment outcomes is unknown. The overarching goal of this project is to provide the first comprehensive description of HHV-8 genome diversity, at the individual and population level, and to evaluate the association of HHV-8 polymorphisms with disease state and therapeutic response. Using state-of-the-art molecular technologies, we propose to determine sequence diversity over the whole HHV-8 genome in specimens from well-annotated cohorts of HHV-8/HIV-1 co-infected persons with and without KS in Uganda. In Aim 1, we will comprehensively characterize HHV-8 diversity to define common polymorphisms and phylogenetic groupings across the cohort population. In Aim 2, we will perform single-genome sequence analysis of polymorphic HHV-8 regions in additional paired oral, plasma and tumor specimens within individuals to determine whether multiple viral variants coexist and whether there is compartmentalization of variants in different anatomic sites. In Aim 3, we will explore associations of HHV-8 polymorphisms with KS disease state and treatment outcomes to identify polymorphisms with potential biologic significance, which may ultimately serve as predictive or treatment-selective biomarkers or targets of therapy.